eDNA Metabarcoding Reveals Diel Connectivity Dynamics of Fish Communities in Xincun Lagoon, Hainan

Coastal lagoons are crucial transitional zones connecting land and sea, and their ecological connectivity with adjacent open waters directly sustains regional biodiversity and ecosystem functions. However, how lagoon fish communities connect on a diurnal timescale remains poorly understood. In this study, we selected Xincun Lagoon on the southeastern coast of Hainan Island, China, as the study area. We established six sampling stations along an environmental gradient from the lagoon interior, through the tidal inlet, to the open sea, and conducted repeated diurnal sampling at six time points on 24 January 2024. Using eDNA metabarcoding, we analyzed the spatiotemporal dynamics of fish communities to examine spatial functional differentiation within the lagoon ecosystem and the potential corridor role of the tidal inlet. Our results showed clear spatial functional differentiation of fish communities along the environmental gradient. The lagoon inlet (XC4) exhibited the highest rate of community temporal change and the greatest amplitude of diversity fluctuation, with a peak change rate of 0.854 during the evening period (18:00–21:00). Its coefficient of variation for Shannon diversity was 6.2 times that of the mangrove creek (XC3). The mangrove creek area (XC3) had the highest Shannon diversity and the smallest fluctuations, functioning as a biodiversity hotspot and a region of relatively stable community structure. Within the lagoon interior, the temporal dynamics at the marginal zone (XC1) were substantially stronger than those in the central zone (XC2). Offshore stations indicated that the ecological influence of the lagoon extended to the 5 m isobath but weakened at the 10 m isobath. Furthermore, Clupeidae eDNA signals were strongest inside the lagoon during the day, at the tidal inlet in the evening, and in offshore waters at night. This study demonstrates the utility of eDNA metabarcoding for capturing fine-scale diel variation in fish community composition and distribution across the lagoon–inlet–offshore gradient, providing information that is difficult to obtain through conventional surveys. These patterns suggest, rather than confirm, that the tidal inlet may play an important role as a corridor linking lagoon and offshore habitats, and provide a reference case for using eDNA technology to study fine-scale connectivity in similar systems.